Ultrafast Protein Dynamics Probed by Site Specific Transient IR Spectroscopy

2020 ◽  
Author(s):  
Christopher R. Hall ◽  
Jinnette Tolentino Collado ◽  
James N. Iuliano ◽  
Katrin Adamczyk ◽  
Andras Lukacs ◽  
...  
Keyword(s):  
Ir Spectroscopy ◽  
Protein Dynamics ◽  
Site Specific

scholarly journals Site-specific 2D IR spectroscopy: a general approach for the characterization of protein dynamics with high spatial and temporal resolution

2019 ◽  
Vol 21 (2) ◽  
pp. 780-788 ◽  
Author(s):  
Sashary Ramos ◽  
Rachel E. Horness ◽  
Jessica A. Collins ◽  
David Haak ◽  
Megan C. Thielges
Keyword(s):  
Ir Spectroscopy ◽  
Spatial Heterogeneity ◽  
Protein Dynamics ◽  
Temporal Resolution ◽  
Protein Structures ◽  
Side Chains ◽  
Conformational Heterogeneity ◽  
Site Specific ◽  
2D Ir

The conformational heterogeneity and dynamics of protein side chains contribute to function, but investigating exactly how is hindered by experimental challenges arising from the fast timescales involved and the spatial heterogeneity of protein structures.

scholarly journals Site-specific Protein Dynamics in Communication Pathway from Sensor to Signaling Domain of Oxygen Sensor Protein, HemAT-Bs

2012 ◽  
Vol 287 (24) ◽  
pp. 19973-19984 ◽  
Author(s):  
Samir F. El-Mashtoly ◽  
Minoru Kubo ◽  
Yuzong Gu ◽  
Hitomi Sawai ◽  
Satoru Nakashima ◽  
...  
Keyword(s):  
Protein Dynamics ◽  
Oxygen Sensor ◽  
Specific Protein ◽  
Site Specific ◽  
Sensor Protein ◽  
Signaling Domain ◽  
Communication Pathway

scholarly journals Direct Observation of Peptide Hydrogel Self-Assembly

2021 ◽  
Author(s):  
Zoë Adams ◽  
Erika Olson ◽  
Zhengwen Lian ◽  
Audrey Kim ◽  
Matthew Holcomb ◽  
...  
Keyword(s):  
Ir Spectroscopy ◽  
Rapid Change ◽  
Stopped Flow ◽  
Side Chains ◽  
Ir Absorption ◽  
Hydrophobic Region ◽  
Site Specific ◽  
Self Assembling ◽  
Wide Range ◽  
Peptide Hydrogel

The characterization of self-assembling molecules presents significant experimental challenges, especially when associated with phase separation or precipitation. Transparent window infrared (IR) spectroscopy leverages site-specific probes that absorb in the “transparent window” region of the biomolecular IR spectrum. Carbon-deuterium (C-D) bonds are especially compelling transparent window probes since they are non-perturbative, can be readily introduced site selectively into peptides and proteins, and their stretch frequencies are sensitive to changes in the local molecular environment. Importantly, IR spectroscopy can be applied to a wide range of molecular samples regardless of solubility or physical state, making it an ideal technique for addressing the solubility challenges presented by self-assembling molecules. Here, we present the first continuous observation of transparent window probes following stopped-flow initiation. To demonstrate utility in a self-assembling system, we selected the MAX1 peptide hydrogel, a biocompatible material that has significant promise for use in tissue regeneration and drug delivery. C-D labeled valine was synthetically introduced into five distinct positions of the twenty-residue MAX1 β-hairpin peptide. Consistent with current structural models, steady-state IR absorption frequencies and linewidths of C-D bonds at all labeled positions indicate that these side chains occupy a hydrophobic region of the hydrogel and that the motion of side chains located in the middle of the hairpin is more restricted than those located on the hairpin ends. Following a rapid change in ionic strength to initiate gelation, the peptide absorption spectra were monitored as function of time, allowing determination of site-specific time constants. We find that within the experimental resolution, MAX1 gelation occurs as a cooperative process. These studies suggest that stopped-flow transparent window FTIR can be extended to other time-resolved applications, such as protein folding and enzyme kinetics.

scholarly journals Site-Specific Protein Dynamics Probed by Ultrafast Infrared Spectroscopy of a Noncanonical Amino Acid

2019 ◽  
Vol 123 (45) ◽  
pp. 9592-9597 ◽  
Author(s):  
Christopher R. Hall ◽  
Jinnette Tolentino Collado ◽  
James N. Iuliano ◽  
Agnieszka A. Gil ◽  
Katrin Adamczyk ◽  
...  
Keyword(s):  
Infrared Spectroscopy ◽  
Amino Acid ◽  
Protein Dynamics ◽  
Specific Protein ◽  
Site Specific ◽  
Noncanonical Amino Acid ◽  
Ultrafast Infrared

Tyrosine as a Non-perturbing Site-Specific Vibrational Reporter for Protein Dynamics

2017 ◽  
Vol 121 (26) ◽  
pp. 6380-6389 ◽  
Author(s):  
Farzaneh Chalyavi ◽  
David G. Hogle ◽  
Matthew J. Tucker
Keyword(s):  
Protein Dynamics ◽  
Site Specific

Multidimensional IR Spectroscopy of Site-Specific Hairpin Folding

2007 ◽  
pp. 350-352
Author(s):  
Adam W. Smith ◽  
Hoi Sung Chung ◽  
Ziad Ganim ◽  
Andrei Tokmakoff
Keyword(s):  
Ir Spectroscopy ◽  
Site Specific

Femtosecond IR spectroscopy: methods and applications to protein dynamics

1994 ◽  
Author(s):  
Philip A. Anfinrud ◽  
Manho Lim ◽  
Timothy A. Jackson
Keyword(s):  
Ir Spectroscopy ◽  
Protein Dynamics
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